self.positions is None

[caillancm@…]

The following bug report has been submitted:
Platform:        Linux-5.3.0-46-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.94 (2020-04-28)
Description
Several large PDBs were open. The message occurred when trying to save a session file. The session file was not written.

This continued to occur even if the offending PDB (which is attached) was closed.

Log:
UCSF ChimeraX version: 0.94.dev202004280056 (2020-04-28)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open2 /home/caillan/rqcH-project/figures/chimerax-
> sessions/200430_H69-comparison_5.cxs

Log from Thu Apr 30 22:46:43 2020UCSF ChimeraX version: 0.94.dev202004280056
(2020-04-28)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open2 /home/caillan/rqcH-project/figures/chimerax-
> sessions/200430_H69-comparison_3.cxs

Log from Thu Apr 30 18:35:55 2020UCSF ChimeraX version: 0.94.dev202004280056
(2020-04-28)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open2 /home/caillan/rqcH-project/figures/chimerax-
> sessions/200429_H69-comparison_2.cxs

Log from Thu Apr 30 14:51:35 2020UCSF ChimeraX version: 0.94.dev202004280056
(2020-04-28)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /home/caillan/rqcH-project/figures/chimerax-
> sessions/200429_H69-comparison_1.cxs format session

Log from Wed Apr 29 19:49:22 2020 Startup Errors  
---  
error | Bundle 'ChimeraX-Registration' custom initialization failed  
warning | Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 432, in initialize  
api._api_caller.initialize(api, session, self)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1652, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/registration/__init__.py", line 41, in initialize  
nag(session)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 28, in nag  
if not check_registration(logger=session.logger):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 49, in check_registration  
return _check_expiration(param, logger)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 131, in _check_expiration  
expires = datetime.strptime(param["Expires"], TimeFormat)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/_strptime.py", line 577, in
_strptime_datetime  
tt, fraction, gmtoff_fraction = _strptime(data_string, format)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/_strptime.py", line 359, in
_strptime  
(data_string, format))  
ValueError: time data 'Tue Apr 13 07:53:02 2021' does not match format '%a %b
%d %H:%M:%S %Y'  
  
UCSF ChimeraX version: 0.94.dev202004280056 (2020-04-28)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open2 /home/caillan/rqcH-project/maps/locally-filtered/rqcH-
> pulldown/LocFilt_EPA-cl7_P-tRNA-YabO_job290.mrc /home/caillan/rqcH-
> project/maps/locally-filtered/rqcH-pulldown/LocFilt_EPA-
> cl1_state-a-1_ws08_job042.mrc /home/caillan/rqcH-project/maps/locally-
> filtered/rqcH-pulldown/LocFilt_EPA-cl6_E-tRNA_job107.mrc /home/caillan/rqcH-
> project/maps/locally-filtered/rqcH-pulldown/LocFilt_EPA-cl4_NFACT-sub-
> cl1_job255.mrc

Opened LocFilt_EPA-cl7_P-tRNA-YabO_job290.mrc, grid size 420,420,420, pixel
0.82, shown at level 0.0179, step 2, values float32  
Opened LocFilt_EPA-cl1_state-a-1_ws08_job042.mrc, grid size 420,420,420, pixel
0.82, shown at level 0.0137, step 2, values float32  
Opened LocFilt_EPA-cl6_E-tRNA_job107.mrc, grid size 420,420,420, pixel 0.82,
shown at level 0.0131, step 2, values float32  
Opened LocFilt_EPA-cl4_NFACT-sub-cl1_job255.mrc, grid size 420,420,420, pixel
0.82, shown at level 0.0122, step 2, values float32  

> set bgColor white

> fitmap #1 inMap #2

Fit map LocFilt_EPA-cl7_P-tRNA-YabO_job290.mrc in map LocFilt_EPA-
cl1_state-a-1_ws08_job042.mrc using 92603 points  
correlation = 0.9928, correlation about mean = 0.8867, overlap = 48.05  
steps = 88, shift = 0.747, angle = 3.64 degrees  
  
Position of LocFilt_EPA-cl7_P-tRNA-YabO_job290.mrc (#1) relative to
LocFilt_EPA-cl1_state-a-1_ws08_job042.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99902582 0.04211214 0.01319019 -9.40718037  
-0.04146702 0.99808671 -0.04586287 14.97699509  
-0.01509634 0.04527124 0.99886066 -5.75176049  
Axis 0.71843756 0.22299119 -0.65887965  
Axis point 0.00000000 129.68876365 319.34624399  
Rotation angle (degrees) 3.63643796  
Shift along axis 0.37098423  
  

> fitmap #3 inMap #2

Fit map LocFilt_EPA-cl6_E-tRNA_job107.mrc in map LocFilt_EPA-
cl1_state-a-1_ws08_job042.mrc using 92558 points  
correlation = 0.9839, correlation about mean = 0.7924, overlap = 32.12  
steps = 80, shift = 0.224, angle = 3.56 degrees  
  
Position of LocFilt_EPA-cl6_E-tRNA_job107.mrc (#3) relative to LocFilt_EPA-
cl1_state-a-1_ws08_job042.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99817648 -0.04948449 0.03456890 2.81264974  
0.04897986 0.99868264 0.01529582 -10.73982101  
-0.03528027 -0.01357474 0.99928526 8.40563374  
Axis -0.23258788 0.56272102 0.79325149  
Axis point 220.23297511 48.58266047 0.00000000  
Rotation angle (degrees) 3.55827866  
Shift along axis -0.02992979  
  

> fitmap #4 inMap #2

Fit map LocFilt_EPA-cl4_NFACT-sub-cl1_job255.mrc in map LocFilt_EPA-
cl1_state-a-1_ws08_job042.mrc using 92559 points  
correlation = 0.9453, correlation about mean = 0.5095, overlap = 25.37  
steps = 68, shift = 0.113, angle = 0.889 degrees  
  
Position of LocFilt_EPA-cl4_NFACT-sub-cl1_job255.mrc (#4) relative to
LocFilt_EPA-cl1_state-a-1_ws08_job042.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99988117 0.00021391 -0.01541426 2.61415103  
-0.00018570 0.99999831 0.00183158 -0.26161214  
0.01541463 -0.00182850 0.99987952 -2.36543899  
Axis -0.11788461 -0.99294389 -0.01287046  
Axis point 154.78437179 0.00000000 168.26245177  
Rotation angle (degrees) 0.88949435  
Shift along axis -0.01795771  
  

> volume #2 level 0.01038

> hide #!3 models

> hide #!4 models

> hide #!1 models

> show #!1 models

> volume #1 level 0.01063

> volume #3 level 0.008931

> volume #4 level 0.006442

> open2 /home/caillan/rqcH-project/modelling/EPA-
> cl1_modelling/200324_cl1-50S-P-tRNA-YabO-RqcH-RSR24-hand-edited-header-
> stripped.pdb

Chain information for 200324_cl1-50S-P-tRNA-YabO-RqcH-RSR24-hand-edited-
header-stripped.pdb #5  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
A | No description available  
B | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
K | No description available  
L | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
  

> hide atoms

> show cartoons

> hide #!2 models

> hide #!4 models

> open2 /home/caillan/rqcH-project/modelling/aligned-pdbs/200418_1vy4-pre-
> attack-cl1-aligned.pdb

Chain information for 200418_1vy4-pre-attack-cl1-aligned.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
B | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 31793, resource id:
56623167, major code: 18 (ChangeProperty), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 31794, resource id:
56623167, major code: 25 (SendEvent), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 31796, resource id:
56623170, major code: 18 (ChangeProperty), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 31797, resource id:
56623170, major code: 25 (SendEvent), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 31799, resource id:
56623173, major code: 18 (ChangeProperty), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 31800, resource id:
56623173, major code: 25 (SendEvent), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 31802, resource id:
56623176, major code: 18 (ChangeProperty), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 31803, resource id:
56623176, major code: 25 (SendEvent), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 31805, resource id:
56623179, major code: 18 (ChangeProperty), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 31806, resource id:
56623179, major code: 25 (SendEvent), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 31814, resource id:
56623182, major code: 18 (ChangeProperty), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 31815, resource id:
56623182, major code: 25 (SendEvent), minor code: 0  

> hide atoms

> hide cartoons

> show cartoons

> hide #!5 models

> show #!1 models

> volume #1 level 0.009274

> volume #1 level 0.01153

> show #!5 models

> hide #!6 models

> hide #!2 models

> save2 /home/caillan/rqcH-project/figures/chimerax-
> sessions/200429_H69-comparison_1.cxs

opened ChimeraX session  

> open2 /home/caillan/rqcH-project/modelling/aligned-pdbs/H69-comparison/pre-
> trans-eco-4v7d-no-ssu.pdb /home/caillan/rqcH-project/modelling/aligned-
> pdbs/H69-comparison/non-rot-tth-APE-tRNAs-4v5d-no-ssu.pdb
> /home/caillan/rqcH-project/modelling/aligned-pdbs/H69-comparison/rot-
> hsa-6y57-no-SSU.pdb

Summary of feedback from opening /home/caillan/rqcH-project/modelling/aligned-
pdbs/H69-comparison/pre-trans-eco-4v7d-no-ssu.pdb  
---  
warnings | Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
1889 messages similar to the above omitted  
  
Summary of feedback from opening /home/caillan/rqcH-project/modelling/aligned-
pdbs/H69-comparison/rot-hsa-6y57-no-SSU.pdb  
---  
warnings | Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
40302 messages similar to the above omitted  
  
Chain information for pre-trans-eco-4v7d-no-ssu.pdb #7  
---  
Chain | Description  
A | No description available  
A | No description available  
B | No description available  
B | No description available  
  
Chain information for non-rot-tth-APE-tRNAs-4v5d-no-ssu.pdb #8  
---  
Chain | Description  
C | No description available  
D | No description available  
D | No description available  
  
Chain information for rot-hsa-6y57-no-SSU.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
D | No description available  
L | No description available  
L | No description available  
S | No description available  
  

> select #9/L:4596@OP1

1 atom, 1 model selected  

> hide sel atoms

> hide sel atoms

> hide sel atoms

> select clear

> hide #!7 models

> hide #!8 models

> hide #!9 models

> show #!9 models

> show #!8 models

> hide #!8 models

> hide #!5,9 atoms

> show #!5,9 cartoons

> hide #!9 models

> show #!8 models

> hide #!8 models

> show #!7 models

> hide #!7 models

> show #!6 models

> show #!4 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!9 models

> hide #!9 models

> show #!6 models

> hide #!5 models

> save2 /home/caillan/rqcH-project/figures/chimerax-
> sessions/200429_H69-comparison_2.cxs

opened ChimeraX session  

> open2 /home/caillan/rqcH-project/modelling/aligned-
> pdbs/H69-comparison/200324_cl1-50S-P-tRNA-YabO-RqcH-RSR24-H69-partial.pdb
> /home/caillan/rqcH-project/modelling/aligned-
> pdbs/H69-comparison/200326_cl4-50S-AP-tRNA-RqcH-H69-partial.pdb
> /home/caillan/rqcH-project/modelling/aligned-
> pdbs/H69-comparison/200326_cl4-50S-AP-tRNA-RqcH-H69-full.pdb
> /home/caillan/rqcH-project/modelling/aligned-
> pdbs/H69-comparison/200324_cl1-50S-P-tRNA-YabO-RqcH-RSR24-H69-full.pdb

Chain information for 200324_cl1-50S-P-tRNA-YabO-RqcH-RSR24-H69-partial.pdb
#10  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
A | No description available  
B | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
K | No description available  
L | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
  
Chain information for 200326_cl4-50S-AP-tRNA-RqcH-H69-partial.pdb #11  
---  
Chain | Description  
0 | No description available  
2 | No description available  
A | No description available  
B | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
K | No description available  
L | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
  
Chain information for 200326_cl4-50S-AP-tRNA-RqcH-H69-full.pdb #12  
---  
Chain | Description  
0 | No description available  
2 | No description available  
A | No description available  
B | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
K | No description available  
L | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
  
Chain information for 200324_cl1-50S-P-tRNA-YabO-RqcH-RSR24-H69-full.pdb #13  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
A | No description available  
B | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
K | No description available  
L | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
  

> hide #!6,10-13 atoms

> show #!6,10-13 cartoons

> select clear

> hide #!12 models

> hide #!11 models

> hide #!10 models

> hide #!13 models

> show #!13 models

> rename #13 cl1-H69-full

> show #!10 models

> hide #!13 models

> rename #10 cl1-H69-partial

> hide #!10 models

> show #!11 models

> rename #14 cl4-H69-partial

> show #!12 models

> hide #!11 models

> rename #11 cl4-H69-partial

> rename #12 cl4-H69-pull

> rename #12 cl4-H69-full

> hide #!12 models

> show #!10 models

> show #!11 models

> hide #!6 models

> hide #!4 models

> show #!13 models

> show #!12 models

> hide #!11 models

> hide #!10 models

> hide #!13 models

> show #!11 models

> hide #!12 models

> show #!2 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!3 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> volume #1 level 0.008937

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> save2 /home/caillan/rqcH-project/figures/chimerax-
> sessions/200430_H69-comparison_3.cxs

opened ChimeraX session  

> hide #!11 models

> show #!8 models

> show #!10 models

> hide #!8,10 atoms

> close #5-9

> open2 /home/caillan/rqcH-project/modelling/aligned-pdbs/H69-comparison/post-
> trans-tth-4v5n-no-ssu.pdb /home/caillan/rqcH-project/modelling/aligned-
> pdbs/H69-comparison/pre-trans-tth-4v5m-no-ssu.pdb /home/caillan/rqcH-
> project/modelling/aligned-pdbs/H69-comparison/post-acc-tth-4v6f-no-ssu.pdb
> /home/caillan/rqcH-project/modelling/aligned-pdbs/H69-comparison/pre-acc-
> tth-4v5g-no-ssu.pdb /home/caillan/rqcH-project/modelling/aligned-
> pdbs/H69-comparison/non-rot-eco-4v9d-no-ssu.pdb /home/caillan/rqcH-
> project/modelling/aligned-pdbs/H69-comparison/rot-eco-4v9d-no-ssu.pdb

Summary of feedback from opening /home/caillan/rqcH-project/modelling/aligned-
pdbs/H69-comparison/post-trans-tth-4v5n-no-ssu.pdb  
---  
warnings | Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
848 messages similar to the above omitted  
  
Summary of feedback from opening /home/caillan/rqcH-project/modelling/aligned-
pdbs/H69-comparison/pre-trans-tth-4v5m-no-ssu.pdb  
---  
warnings | Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
848 messages similar to the above omitted  
  
Summary of feedback from opening /home/caillan/rqcH-project/modelling/aligned-
pdbs/H69-comparison/pre-acc-tth-4v5g-no-ssu.pdb  
---  
warnings | Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
Duplicate atom serial number found: 99999  
3293 messages similar to the above omitted  
  
Chain information for post-trans-tth-4v5n-no-ssu.pdb #5  
---  
Chain | Description  
A | No description available  
A | No description available  
B | No description available  
B | No description available  
  
Chain information for pre-trans-tth-4v5m-no-ssu.pdb #6  
---  
Chain | Description  
A | No description available  
A | No description available  
B | No description available  
B | No description available  
  
Chain information for post-acc-tth-4v6f-no-ssu.pdb #7  
---  
Chain | Description  
A | No description available  
A | No description available  
B | No description available  
  
Chain information for pre-acc-tth-4v5g-no-ssu.pdb #8  
---  
Chain | Description  
A | No description available  
A | No description available  
B | No description available  
B | No description available  
  
Chain information for non-rot-eco-4v9d-no-ssu.pdb #9  
---  
Chain | Description  
B | No description available  
D | No description available  
D | No description available  
  
Chain information for rot-eco-4v9d-no-ssu.pdb #14  
---  
Chain | Description  
A | No description available  
A | No description available  
C | No description available  
C | No description available  
  

> hide #!5-10,14 atoms

> hide #!2 models

> hide #!1 models

Drag select of 64 residues  

> select up

322534 atoms, 361228 bonds, 5 models selected  

> color sel skyblue

> select clear

Drag select of 84 residues  

> select up

387236 atoms, 433689 bonds, 6 models selected  

> color sel lightgrey

> select clear

> save2 /home/caillan/rqcH-project/figures/chimerax-
> sessions/200430_H69-comparison_4.cxs

> hide #!14 models

> hide #!10 models

> color #5 tan

> color #6 plum

> color #7 lightgreen

> color #8 salmon

> color #9 deeppink

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> show #!2 models

> show #!10 models

> color #10 grey

> color #10/A/B lightgrey

> color #10/0 darkviolet

> color #10/1 gold

> color #10/2 skyblue

> select clear

> hide #!2 models

> name #10/A:1935-1955 cl1-H69-part

"cl1-H69-part": invalid atom specifier  

> name cl1-H69-part #10/A:1935-1955

> show cl1-H69-part atoms

> nucleotides #!10 atoms

> style nucleic & #!10 stick

Changed 64453 atom styles  

> show #!2 models

> save2 /home/caillan/rqcH-project/figures/chimerax-
> sessions/200430_H69-comparison_4.cxs

> volume #2 step 1

> hide #!2 models

> select #10/1:11

11 atoms, 10 bonds, 1 model selected  

> select clear

> show #!1 models

> show #!2 models

> hide #!1 models

> show #!4 models

> hide #!4 models

> show #!11 models

> hide #!11 models

> show #!8 models

> hide #!8 models

> show #!9 models

> hide #!9 models

> show #!7 models

> hide #!7 models

> show #!6 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> color #10/A grey

> volume #2 color #bfadad

> volume #2 color #b09f9f

> volume #2 color #b0a6a6

> volume #2 color #b9aeae

> volume #2 color #b9b9b9

> volume #2 color #c7c7c7

> volume #2 color #c6c6c6

> volume #2 color #c5c5c5

> volume #2 color #c4c4c4

> volume #2 color #c3c3c3

> volume #2 color #c2c2c2

> volume #2 color #c2c1c1

> volume #2 color #bab9b9

> volume #2 color #b5b3b3

> volume #2 color #b3b1b1

> volume #2 color #b3b2b2

> volume #2 color #b4b3b3

> volume #2 color #b4b4b4

> volume #2 color #b5b5b5

> volume #2 color #b8b8b8

> volume #2 color #bababa

> volume #2 color #bababafb

> volume #2 color #bababac0

> volume #2 color #bababa06

> volume #2 color #bababa04

> volume #2 color #bababa07

> volume #2 color #bababa17

> volume #2 color #bababa19

> volume #2 color #bababa28

> volume #2 color #bababa2d

> volume #2 color #bababa2e

> volume #2 color #bababa38

> volume #2 color #bababa3d

> volume #2 color #bababa3e

> volume #2 color #bababa44

> volume #2 color #bababa45

> volume #2 color #bababa47

> volume #2 color #bababa4b

> volume #2 color #bababa4f

> volume #2 color #bababa4e

> volume #2 color #bababa4d

> volume #2 color #bababa4c

> volume #2 color #bababa4a

> volume #2 color #bababa5f

> volume #2 color #bababa74

> volume #2 color #bababa79

> volume #2 color #bababa7a

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> hide cl1-H69-part atoms

> volume #!2 style mesh

> toolshed show "Side View"

> toolshed show "Side View"

> hide #!2 models

> show #!2 models

> hide #!2 models

> select #10/2:28

20 atoms, 21 bonds, 1 model selected  

> select up

1563 atoms, 1744 bonds, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> show cl1-H69-part atoms

> color cl1-H69-part byhetero

> select clear

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #!2 style surface

> hide #!2 models

> show #!2 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> pwd

Current working directory is: /home/caillan  

> cd /home/caillan/rqcH-project/figures

Current working directory is: /home/caillan/Dropbox/rqcH-project/figures  

> cd /home/caillan/rqcH-project/figures/H69-comp/close-panels

Current working directory is: /home/caillan/Dropbox/rqcH-
project/figures/H69-comp/close-panels  

> save 200430_cl1-part-w-density_1.png width 800 height 600
> transparentBackground true

> hide #10.1 models

> volume #2 color #bfbbbb

> volume #2 color #c0bcbc

> volume #2 color #c0bfbf

> volume #2 color silver

> volume #2 color #c0c0c0fd

> volume #2 color #c0c0c0ca

> volume #2 color #c0c0c07c

> volume #2 color #c0c0c07b

> volume #2 color #c0c0c04f

> volume #2 color #c0c0c02c

> volume #2 color #c0c0c027

> volume #2 color #c0c0c026

> volume #2 color #c0c0c025

> volume #2 color #c0c0c021

> volume #2 color #c0c0c016

> volume #2 color #c0c0c012

> volume #2 color #c0c0c00c

> volume #2 color #c0c0c00b

> volume #2 color #c0c0c00f

> volume #2 color #c0c0c010

> volume #2 color #c0c0c011

> volume #2 color #c0c0c012

> volume #2 color #c0c0c011

> volume #2 color #c0c0c00f

> volume #2 color #c0c0c010

> volume #2 color #c0c0c012

> volume #2 color #c0c0c014

> volume #2 color #c0c0c015

> save 200430_cl1-part-w-density_1.png width 800 height 600
> transparentBackground true

> volume #2 color #bfbbbb

> volume #2 color #c5c1c1

> volume #2 color #c5c0c0

> volume #2 color #c3bebe

> volume #2 color #c1bdbd

> volume #2 color #c1bfbf

> volume #2 color #c3c0c0

> volume #2 color #c3c1c1

> volume #2 color #c3c3c3

> volume #2 color #c4c4c4

> volume #2 color #c5c5c5

> volume #2 color #c5c5c522

> volume #2 color #c5c5c521

> volume #2 color #c5c5c523

> volume #2 color #c5c5c53a

> volume #2 color #c5c5c554

> volume #2 color #c5c5c568

> volume #2 color #c5c5c569

> volume #2 color #c5c5c568

> volume #2 color #c5c5c558

> volume #2 color #c5c5c528

> volume #2 color #c5c5c527

> volume #2 color #c5c5c526

> save 200430_cl1-part-w-density_1.png width 800 height 600
> transparentBackground true

> save 200430_cl1-part-w-density_1.png width 800 height 600
> transparentBackground true

> save 200430_cl1-part-w-density_1.png width 800 height 600
> transparentBackground true

> volume #2 color #bfb8b8

> volume #2 color #b8b0b0

> volume #2 color #b8b1b1

> volume #2 color #b9b2b2

> volume #2 color #b9b4b4

> volume #2 color #beb9b9

> volume #2 color #bebaba

> volume #2 color #bfbbbb

> volume #2 color #bfbcbc

> volume #2 color #c1bfbf

> volume #2 color #c1c0c0

> volume #2 color #c1c1c1

> volume #2 color #c1c1c18e

> volume #2 color #c1c1c18f

> volume #2 color #c1c1c19a

> volume #2 color #c1c1c19c

> volume #2 color #c1c1c1d2

> volume #2 color #c1c1c1d3

> volume #2 color #c1c1c1d1

> volume #2 color #c1c1c1a0

> volume #2 color #c1c1c197

> volume #2 color #c1c1c190

> volume #2 color #c1c1c17b

> volume #2 color #c1c1c15e

> volume #2 color #c1c1c15c

> volume #2 color #c1c1c159

> volume #2 color #c1c1c158

> volume #2 color #c1c1c159

> volume #2 color #c1c1c15a

> volume #2 color #c1c1c15d

> volume #2 color #c1c1c15e

> volume #2 color #c1c1c15f

> volume #2 color #c1c1c160

> volume #2 color #c1c1c164

> volume #2 color #c1c1c165

> volume #2 color #c1c1c166

> save 200430_cl1-part-w-density_1.png width 800 height 600
> transparentBackground true

> view name H69-close

> view lsit

Expected an objects specifier or a view name or a keyword  

> view list

Named views: H69-close  

> hide #2

> save 200430_cl1-part-model_1.png width 800 height 600 transparentBackground
> true

> save 200430_cl1-part-model_1.png width 800 height 600 transparentBackground
> true

> save 200430_cl1-part-model_1.png width 800 height 600 transparentBackground
> true

> save 200430_cl1-part-density_1.png width 800 height 600
> transparentBackground true

> view name H69-close

> hide #!10 atoms

> show #!5 models

> select #5/A:20

50 atoms, 52 bonds, 1 model selected  

> select clear

> select #5/A:17

48 atoms, 49 bonds, 1 model selected  

> select up

1922 atoms, 2140 bonds, 1 model selected  

> color sel lightgreen

> select clear

> select #5/A:579

9 atoms, 8 bonds, 1 model selected  

> select up

134 atoms, 134 bonds, 1 model selected  

> select up

7149 atoms, 7471 bonds, 1 model selected  

> select clear

> view list

Named views: H69-close  

> view H69-close

> hide #!10 models

Drag select of 11 residues  

> hide sel cartoons

> save2 /home/caillan/rqcH-project/figures/chimerax-
> sessions/200430_H69-comparison_5.cxs

opened ChimeraX session  

> cartoon style width 2.2 thickness 1

> view list

Named views: H69-close  

> view H69-close

> select up

1870 atoms, 2089 bonds, 1 model selected  

> select up

7149 atoms, 7471 bonds, 1 model selected  

> select clear

> hide #!5 models

> show #!10 models

> save 200430_cl1-part-model_2.png width 800 height 600 transparentBackground
> true

> cd /home/caillan/rqcH-project/figures/H69-comparison/clode-view/

[Errno 2] No such file or directory: '/home/caillan/rqcH-
project/figures/H69-comparison/clode-view/'  

> cd /home/caillan/rqcH-project/figures/

Current working directory is: /home/caillan/Dropbox/rqcH-project/figures  

> cd H69-comp/close-panels

Current working directory is: /home/caillan/Dropbox/rqcH-
project/figures/H69-comp/close-panels  

> save 200430_cl1-part-model_2.png width 800 height 600 transparentBackground
> true

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> save 200430_cl1-part-model_2.png width 800 height 600 transparentBackground
> true

> color #10/A/B lightgrey

> save 200430_cl1-part-model_2.png width 800 height 600 transparentBackground
> true

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting flat

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> save 200430_cl1-part-model_2.png width 800 height 600 transparentBackground
> true

> show #!2 models

> save 200430_cl1-part-density-model_2.png width 800 height 600
> transparentBackground true

> view list

Named views: H69-close  

> view name H69-close

> hide #!2 models

> view orient

> view H69-close

> toolshed show "Side View"

> show #!2 models

> save 200430_cl1-part-density-model_2-alt.png width 800 height 600
> transparentBackground true

> hide #!2 models

> view H69-close

> show #!5 models

> select up

Nothing selected  

> save 200430_cl1-post-trans_4v5n_2.png width 800 height 600
> transparentBackground true

> hide #!10 models

Drag select of 26 residues  

> select clear

Drag select of 22 residues  

> color sel pink

> select clear

> view H69-close

> show #!1 models

> hide #!1 models

> show #!10 models

> save 200430_cl1-post-trans_4v5n_2.png width 800 height 600
> transparentBackground true

> hide #10/1/2/0 cartoons

> save 200430_cl1-post-trans_4v5n_2.png width 800 height 600
> transparentBackground true

> hide #!5 models

> show #!9 models

> show #9 cartoons

> show #!9 cartoons

> close #9

> save2 /home/caillan/rqcH-project/figures/chimerax-
> sessions/200430_H69-comparison_5.cxs

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1285, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 815, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 566, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x7f8dadc25f10>
-> <chimerax.atomic.structure.AtomicStructure object at 0x7f8e337d9390> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> -> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1285, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1513, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 90, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 101, in show_save_file_dialog  
_dlg.display(session, session.ui.main_window)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 31, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 815, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 566, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x7f8dadc25f10>
-> <chimerax.atomic.structure.AtomicStructure object at 0x7f8e337d9390> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> -> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  

> save2 /home/caillan/rqcH-project/figures/chimerax-
> sessions/200430_H69-comparison_5.cxs

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1285, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 815, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 566, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x7f8dadc25f10>
-> <chimerax.atomic.structure.AtomicStructure object at 0x7f8e337d9390> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> -> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1285, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1513, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 90, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 101, in show_save_file_dialog  
_dlg.display(session, session.ui.main_window)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 31, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 815, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 566, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x7f8dadc25f10>
-> <chimerax.atomic.structure.AtomicStructure object at 0x7f8e337d9390> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> -> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  

> save2 /home/caillan/rqcH-project/figures/chimerax-
> sessions/200430_H69-comparison_6.cxs

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1285, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 815, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 566, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x7f8dadc25f10>
-> <chimerax.atomic.structure.AtomicStructure object at 0x7f8e337d9390> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> -> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1285, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1513, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 90, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 101, in show_save_file_dialog  
_dlg.display(session, session.ui.main_window)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 31, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 815, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 566, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x7f8dadc25f10>
-> <chimerax.atomic.structure.AtomicStructure object at 0x7f8e337d9390> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> -> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  

> close #14

> save2 /home/caillan/rqcH-project/figures/chimerax-
> sessions/200430_H69-comparison_6.cxs

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1285, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 815, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 566, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x7f8dadc25f10>
-> <chimerax.atomic.structure.AtomicStructure object at 0x7f8e337d9390> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> -> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1285, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1513, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 90, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 101, in show_save_file_dialog  
_dlg.display(session, session.ui.main_window)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 31, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 815, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 566, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x7f8dadc25f10>
-> <chimerax.atomic.structure.AtomicStructure object at 0x7f8e337d9390> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> -> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  

> view name H69-close

> save2 /home/caillan/rqcH-project/figures/chimerax-
> sessions/200430_H69-comparison_6.cxs

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1285, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 815, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 566, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x7f8dadc25f10>
-> <chimerax.atomic.structure.AtomicStructure object at 0x7f8e337d9390> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> -> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1285, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1513, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 90, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 101, in show_save_file_dialog  
_dlg.display(session, session.ui.main_window)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 31, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 815, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 566, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x7f8dadc25f10>
-> <chimerax.atomic.structure.AtomicStructure object at 0x7f8e337d9390> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> -> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  

> save2 /home/caillan/rqcH-project/figures/chimerax-
> sessions/200430_H69-comparison_6.cxs

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1285, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 815, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 566, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x7f8dadc25f10>
-> <chimerax.atomic.structure.AtomicStructure object at 0x7f8e337d9390> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> -> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1285, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1513, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 90, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 101, in show_save_file_dialog  
_dlg.display(session, session.ui.main_window)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 31, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 815, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 566, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x7f8dadc25f10>
-> <chimerax.atomic.structure.AtomicStructure object at 0x7f8e337d9390> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> -> 'non-
rot-eco-4v9d-no-ssu.pdb'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  




OpenGL version: 4.5 (Core Profile) Mesa 19.2.8
OpenGL renderer: Mesa DRI Intel(R) UHD Graphics 620 (Kabylake GT2) 
OpenGL vendor: Intel Open Source Technology Center
Manufacturer: LENOVO
Model: 20L6S01W00
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz
Cache Size: 6144 KB
Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 [8086:5917] (rev 07)
	Subsystem: Lenovo UHD Graphics 620 [17aa:225d]
	Kernel driver in use: i915
File attachment: non-rot-eco-4v9d-no-ssu.pdb

non-rot-eco-4v9d-no-ssu.pdb​

[caillancm@…]

Added by email2trac

[Eric Pettersen]

Reported by Cailan Crowe-McAuliffe

[Tom Goddard]

A NucleotideState object is trying to save a reference to an AtomicStructure that was closed. This has been reported 5 times so far and causes the user to lose their work since they can no longer save a session. There must be a case where NucleotideState does not clean-up when its AtomicModel closes.

[Greg Couch]

Duplicate of #2955. Finally able to reproduce and fix.